Variant report

Variant	rs2290545
Chromosome Location	chr3:46967040-46967041
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:46966327-46969602	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:46966735-46970133	GM12878	blood:	n/a	n/a
3	MTA3	chr3:46966876-46970269	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:46966700-46969363	GM18951	blood:	n/a	n/a
5	POLR2A	chr3:46967011-46969467	GM12891	blood:	n/a	n/a
6	POLR2A	chr3:46966650-46969522	GM12891	blood:	n/a	n/a
7	POLR2A	chr3:46956505-46971093	K562	blood:	n/a	n/a
8	POLR2A	chr3:46966882-46970456	GM12891	blood:	n/a	n/a
9	POLR2A	chr3:46966435-46970329	GM18505	blood:	n/a	n/a
10	POLR2A	chr3:46966857-46969609	GM12892	blood:	n/a	n/a
11	POLR2A	chr3:46966326-46969534	GM12892	blood:	n/a	n/a
12	POLR2A	chr3:46966321-46967319	K562	blood:	n/a	n/a
13	POLR2A	chr3:46966461-46969470	GM12892	blood:	n/a	n/a
14	POLR2A	chr3:46966406-46968245	A549	lung:	n/a	n/a
15	POLR2A	chr3:46966707-46970065	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:46966311-46969582	GM12892	blood:	n/a	n/a
17	POLR2A	chr3:46966428-46967872	Hela-S3	cervix:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:46967009..46980239-chr3:47015804..47024437,23	MCF-7	breast:
2	chr3:46966733..46968938-chr3:47035742..47038273,2	K562	blood:
3	chr3:46966739..46968792-chr3:46972024..46974475,2	K562	blood:
4	chr3:46967003..46969518-chr3:47029296..47031281,2	K562	blood:
5	chr3:46967003..46969094-chr3:47027907..47030796,2	K562	blood:
6	chr3:46966170..46968321-chr3:47021061..47023040,2	K562	blood:
7	chr3:46965883..46969429-chr3:47022291..47025425,4	MCF-7	breast:
8	chr3:46966646..46969252-chr3:47031389..47034280,2	MCF-7	breast:

No data

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160799	Chromatin interaction
ENSG00000160796	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1001284	0.84[ASN][1000 genomes]
rs10865943	0.89[ASN][1000 genomes]
rs1138518	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11705936	0.88[ASN][1000 genomes]
rs11719795	0.86[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.88[ASN][1000 genomes]
rs1466275	0.82[ASN][1000 genomes]
rs2168443	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs2242116	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2290546	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4539969	0.82[ASN][1000 genomes]
rs4587	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs4682845	0.89[ASN][1000 genomes]
rs4683296	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683297	0.83[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs4683298	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4683299	0.87[ASN][1000 genomes]
rs4683300	0.83[ASN][1000 genomes]
rs4683301	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs6442038	0.83[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs6442039	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442040	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs6780601	0.91[ASN][1000 genomes]
rs724448	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs724449	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs724450	0.91[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7623898	0.90[ASN][1000 genomes]
rs7635480	0.81[ASN][1000 genomes]
rs7645278	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7646906	0.85[ASN][1000 genomes]
rs9852082	0.83[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs9855938	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007449	chr3:46652343-46986578	Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv536554	chr3:46652343-46986578	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	esv2757869	chr3:46680452-46972489	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv2759147	chr3:46680452-46972489	Genic enhancers Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv915922	chr3:46768104-47009805	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv876752	chr3:46879831-46967040	Bivalent/Poised TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv876754	chr3:46884552-46967040	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv460526	chr3:46935527-47001350	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv3800	chr3:46961648-47007241	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2290545	C3orf75	cis	cerebellum	SCAN
rs2290545	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs2290545	HYAL2	cis	cerebellum	SCAN
rs2290545	CCDC12	cis	cerebellum	SCAN
rs2290545	SCAP	cis	cerebellum	SCAN
rs2290545	CCDC12	cis	parietal	SCAN
rs2290545	TMIE	cis	parietal	SCAN
rs2290545	SCAP	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46956600-46967200	Strong transcription	Thymus	Thymus
2	chr3:46957800-46967200	Strong transcription	HSMM	muscle
3	chr3:46958200-46967200	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr3:46958200-46967600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr3:46958200-46968200	Strong transcription	Rectal Mucosa Donor 31	rectum
6	chr3:46958200-46968800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:46958400-46967200	Strong transcription	HMEC	breast
8	chr3:46958400-46967600	Strong transcription	Primary T cells from cord blood	blood
9	chr3:46958400-46967800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:46958400-46968200	Strong transcription	Dnd41	blood
11	chr3:46958600-46967200	Strong transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:46958600-46967400	Strong transcription	Liver	Liver
13	chr3:46958600-46967800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr3:46958600-46968000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:46958600-46970200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr3:46958800-46967200	Strong transcription	NH-A	brain
17	chr3:46958800-46967600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:46958800-46967600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:46958800-46967800	Strong transcription	Osteobl	bone
20	chr3:46959000-46971400	Strong transcription	K562	blood
21	chr3:46959400-46967200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:46959400-46967200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:46959400-46967200	Strong transcription	Brain Angular Gyrus	brain
24	chr3:46959400-46967600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:46959400-46968200	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:46959600-46967400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:46959600-46970600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:46959800-46968000	Strong transcription	Fetal Stomach	stomach
29	chr3:46959800-46969200	Strong transcription	NHEK	skin
30	chr3:46959800-46971200	Strong transcription	Hela-S3	cervix
31	chr3:46960200-46967200	Strong transcription	Ovary	ovary
32	chr3:46960200-46967400	Strong transcription	Brain Substantia Nigra	brain
33	chr3:46960200-46968600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:46960200-46971200	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:46960400-46967200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:46960400-46967200	Strong transcription	Colonic Mucosa	Colon
37	chr3:46960400-46967400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
38	chr3:46960400-46967600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:46960400-46968400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:46960400-46969400	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:46960400-46970400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:46960400-46970400	Strong transcription	Fetal Lung	lung
43	chr3:46960600-46967200	Strong transcription	NHLF	lung
44	chr3:46960600-46969800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:46961000-46970000	Strong transcription	Brain Germinal Matrix	brain
46	chr3:46961200-46968400	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr3:46961400-46970400	Strong transcription	Fetal Brain Female	brain
48	chr3:46961800-46967400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:46961800-46967400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr3:46961800-46971200	Strong transcription	HepG2	liver

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